GonzalezMiranda2013 - The effect of circadian oscillations on biochemical cell signaling by NF-κB

  public model
Model Identifier
BIOMD0000000893
Short description 
This is a mathematical model for NF-κB oscillations, described by a set of ordinary nonlinear differential equations, when perturbed by a circadian oscillation.
Format
SBML (L2V4)
Related Publication
  • On the effect of circadian oscillations on biochemical cell signaling by NF-κB.
  • González-Miranda JM
  • Journal of theoretical biology , 10/ 2013 , Volume 335 , pages: 283-294 , PubMed ID: 23820037
  • Departamento de Física Fundamental, Universidad de Barcelona, Av. Diagonal 647, 08028 Barcelona, Spain. jmgonzalezm@ub.edu
  • We report the results of a numerical investigation of a mathematical model for NF-κB oscillations, described by a set of ordinary nonlinear differential equations, when perturbed by a circadian oscillation. The main result is that a circadian rhythm, even when it represents a weak perturbation, enhances the signaling capabilities of NF-κB oscillations. This is done by turning rest states into periodic oscillations, and periodic oscillations into quasiperiodic oscillations. Strong perturbations result in complex periodic oscillations and even in chaos. Circadian rhythms would then result in a NF-κB dynamics that is more complex than the simple oscillations and rest states, initially reported for this model. This renders it more amenable for information coding.
Contributors
Submitter of the first revision: Johannes Meyer
Submitter of this revision: Rahuman Sheriff
Modellers: Rahuman Sheriff, Johannes Meyer

Metadata information

is (2 statements)
BioModels Database MODEL1912160002
BioModels Database BIOMD0000000893

isDescribedBy (1 statement)
PubMed 23820037

isDerivedFrom (1 statement)
PubMed 16829571

hasProperty (4 statements)
Mathematical Modelling Ontology Ordinary differential equation model
NCIt Biological Rhythm
Experimental Factor Ontology circadian rhythm
NCIt Signaling Pathway

Curation status
Curated
Tags

Connected external resources

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Model files
GonzalezMiranda2013.xml SBML L2V4 Representation of GonzalezMiranda2013 - The effect of circadian oscillations on biochemical cell signaling by NF-κB 28.71 KB Preview | Download

Additional files
GonzalezMiranda2013.cps COPASI file of GonzalezMiranda2013 - The effect of circadian oscillations on biochemical cell signaling by NF-κB 52.03 KB Preview | Download
GonzalezMiranda2013.sedml SED-ML file of GonzalezMiranda2013 - The effect of circadian oscillations on biochemical cell signaling by NF-κB 1.70 KB Preview | Download

  • Model originally submitted by : Johannes Meyer
  • Submitted: Dec 16, 2019 10:11:37 AM
  • Last Modified: Oct 8, 2021 8:03:49 AM
Revisions
  • Version: 5 public model Download this version
    • Submitted on: Oct 8, 2021 8:03:49 AM
    • Submitted by: Rahuman Sheriff
    • With comment: Automatically added model identifier BIOMD0000000893
  • Version: 3 public model Download this version
    • Submitted on: Dec 16, 2019 10:11:37 AM
    • Submitted by: Johannes Meyer
    • With comment: Automatically added model identifier BIOMD0000000893

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
z

C104199 		0.0 item
y

C104199 		0.0 item
x

NF-kB 		0.0 item
Reactions
Reactions Rate Parameters
z => ; x compartment*C*z*(1-x)/(epsilon+z) epsilon = 2.0E-5; C = 0.035
y => compartment*k1*y k1=1.0
=> z; y compartment*y []
=> y; x compartment*x*x []
x => ; z compartment*B*z*x/(delta+x) delta = 0.029; B = 954.5
=> x; z compartment*A*(1-x)/(epsilon+z) A = 0.007; epsilon = 2.0E-5
Curator's comment:
(added: 16 Dec 2019, 10:11:27, updated: 16 Dec 2019, 10:11:27)
Reproduced plot of Figure 4(b) in the original publication. Model simulated and plot produced using COPASI 4.24 (Build 197).